I came across a nice article today by Dennis Fisher on “The Root of the Botnet Epidemic”.

It's the start of what looks like an interesting series on "the roots, growth and effects of the botnet epidemic" and the first aricle takes a historical overview of the situation around the turn of the century, looking at the first DDoS attacks, Mafiaboy, trinoo, stachedraht and all that, and the beginning of "botmaster-friendly" features like Windows interfaces with point-and-click option selection and some telling quotes  from Joe Stewart and Jose Nazario.

We seem to have come a long way since those primitive Linux tools and the introduction of techniques like rate-limiting to shield the backbone from malicious packet storms, but not so far as to encourage complacency.

If you're interested in the historical aspect, here are a couple of references off my bookshelf that you might find of interest:

"Chapter 4: Big Bad Botnets" in the "AVIEN Malware Defense Guide" (ed. Harley, Syngress 2007)

"Botnets: the Killer Web App" (ed. Schiller & Binkley, Syngress 2007)

Plus: "Net of the Living Dead: Bots, Botnets and Zombies" (Harley, Lee; 2008)

David Harley 
Director of Malware Intelligence